def main():
"""
basically it verifies the options and conf_dict first, then loop_xvgs,
passing whatever should be parsed, ugly code!!! aaaaaahhh....
"""
args = parse_cmd()
# Verify the iterms in args
conf = args.conf
if not os.path.exists(conf):
raise IOError("{0} cannot found".format(conf))
conf_dict = ConfigObj(conf)
SEQS, CDTS, TMPS, NUMS = argparse_action.get_sctn(args, conf_dict['system'])
h5filename = conf_dict['data']['h5filename']
title = conf_dict['data']['title']
# About the property
ppty = args.ppty
p_conf = conf_dict['properties'][ppty] # property configuration
property_obj = h5t.Property(ppty) # including table desc & schema
try:
ogd = p_conf['ogd'] # contains xvg_name and table_name patterns
except KeyError:
print "#" * 20
print '"ogd" not specified in {0} in {1}'.format(ppty, conf)
print "#" * 20
sys.exit(1)
if not args.nobk:
backup_file(h5filename) # later when this script matures, this step may not be necessary
# Start dealing with the h5 file now
h5file = tables.openFile(h5filename, mode="a", title=title)
filters = tables.Filters(complevel=8, complib='zlib')
# zx_create_group is redundant and ugly code, I amd looking for a way to
# overwrite creatGroup in table.file.File 2012-03-16
ppty_group = zx_create_group(h5file, '/', ppty, filters=filters, title=property_obj.desc) # property group
ogd_group = zx_create_group(h5file, ppty_group._v_pathname, 'ogd', filters)
ogd_path = ogd_group._v_pathname # should == ogd_path = os.path.join('/', ppty, 'ogd')
# loop through xvg files and create a table for each one
# ugly code!!! aaaaaahhh Should I learn loop? and make it more clear!
# parsing so many args are really confusing
loop_xvgs(SEQS, CDTS, TMPS, NUMS,
ppty, h5file, property_obj, ogd, ogd_path
)
def main():
args = parse_cmd()
# initialization YOU DIAN LUANG!
conf = args.conf
if not os.path.exists(conf):
raise IOError("{0} cannot found".format(conf))
conf_dict = ConfigObj(conf)
SEQS, CDTS, TMPS, NUMS = get_sctn(args, conf_dict['systems'])
h5filename = conf_dict['data']['h5filename']
if not os.path.exists(h5filename):
raise IOError("{0} cannot found".format(h5filename))
ppty = args.ppty
tpostproc = args.tpostproc # type of postprocess. i.e. ave, alx
tpostproc_kwargs = conf_dict['postprocess'][tpostproc]
rootUEP = os.path.join('/', ppty)
# start dealing with the h5 file
h5file = tables.openFile(h5filename, 'a', rootUEP=rootUEP)
tpostproc_group_path = os.path.join('/', tpostproc)
if h5file.__contains__(tpostproc_group_path):
tpostproc_group = h5file.getNode(h5file.root, tpostproc)
else:
# meaning it's the first time to run tpostproc postprocess for this ppty
tpostproc_group = h5file.createGroup(h5file.root, tpostproc)
if args.tpostproc in ['ave', 'ave10']:
loop_h5_ave(SEQS, CDTS, TMPS, NUMS, h5file, ppty, tpostproc_group, tpostproc_kwargs)
if args.tpostproc == 'alx':
loop_h5_alx(SEQS, CDTS, TMPS, NUMS, h5file, ppty, tpostproc_group, tpostproc_kwargs)
def main():
# determine which function to call
g_tool, args = gai.target_the_type_of_analysis()
g_tool_name = g_tool.func_name # directory will be named after func_name
config_file = args.config_file
if not os.path.exists(config_file):
raise ValueError('configuration file: {0} may not exist!'.format(config_file))
config_dict = ConfigObj(config_file)
SEQS, CDTS, TMPS, NUMS = aa.get_sctn(args, config_dict['system'])
dirchy_dict = config_dict['dirchy']
directory_hierarchy = dirchy(SEQS, CDTS, TMPS, NUMS, dirchy_dict)
# confirm outpudir path, if not specified either in cmd or in the
# configuration file, 'R_OUTPUT" will be used in the current directory
# to avoid scinet crash.
if args.outputdir:
outputdir = args.outputdir
elif config_dict['data'].has_key('outputdir'):
v = config_dict['data']['outputdir']
if len(v) > 0 and v: # make sure v is not '' or None
outputdir = v
else:
outputdir = 'R_OUTPUT'
else:
outputdir = 'R_OUTPUT'
if not os.path.exists(outputdir):
os.mkdir(outputdir)
# parent_logd holds all the logs which keep the output of analysis tools
parent_logd = os.path.join(outputdir, 'LOGS')
# just mkdir parent_logd no matter testing or not
if not os.path.exists(parent_logd):
os.mkdir(parent_logd)
logd = os.path.join(
outputdir, 'LOGS', '{0}_log'.format(g_tool_name)
) if not args.nolog else None
if logd and not os.path.exists(logd):
os.mkdir(logd)
# now you have g_tool, g_tool_name, outputdir, logd, directory_hierarchy
x = gen_input_args(g_tool, g_tool_name, outputdir, logd, directory_hierarchy,
args.test, args.cdb, args.toa, args.btime, args.etime, args.dt,
config_dict)
gai.runit(x, args.numthread, args.test)
separator = "#" * 79
print separator
dd = args.__dict__
# update variables that are read from the config file
dd['SEQS'] = SEQS
dd['CDTS'] = CDTS
dd['TMPS'] = TMPS
dd['NUMS'] = NUMS
for k in sorted(dd):
print "{0:>20s}:{1}".format(k, dd[k])
print separator